Alignments for a candidate for astD in Shewanella sp. ANA-3

GapMind for catabolism of small carbon sources

Alignments for a candidate for astD in Shewanella sp. ANA-3

Align Succinylglutamic semialdehyde dehydrogenase (EC 1.2.1.71) (characterized)
to candidate 7023382 Shewana3_0612 succinylglutamic semialdehyde dehydrogenase (RefSeq)

Query= reanno::MR1:199807
         (487 letters)



>FitnessBrowser__ANA3:7023382
          Length = 487

 Score =  935 bits (2416), Expect = 0.0
 Identities = 466/486 (95%), Positives = 476/486 (97%)

Query: 1   MTHFIKGQWHTGKGHDVASSNPANGEIIWRGQTATAEQVNAAVDAAREAQFDWFILGFDA 60
           MTHFIKGQW  GKGHDV SSNPAN EIIWRGQTATAEQVNAAVDAAREAQFDWF+LGFD 
Sbjct: 1   MTHFIKGQWQAGKGHDVTSSNPANSEIIWRGQTATAEQVNAAVDAAREAQFDWFMLGFDG 60

Query: 61  RLKIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSASAYNKRTGTET 120
           RLKIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSA+AYNKRTGTE 
Sbjct: 61  RLKIVEAYRSQLEANKAELAETIAQETGKPQWETATEVAAMIGKIGLSATAYNKRTGTEA 120

Query: 121 NDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNSVVFKPSELTPKVAELM 180
           NDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGN+VVFKPSELTPKVAELM
Sbjct: 121 NDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIVPALLAGNTVVFKPSELTPKVAELM 180

Query: 181 VTLWEKSGLPAGVLNLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL 240
           V+LWEK+GLPAGV+NLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL
Sbjct: 181 VSLWEKAGLPAGVINLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYAGHPGKIL 240

Query: 241 ALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKLVE 300
           ALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKLVE
Sbjct: 241 ALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKLVE 300

Query: 301 AVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQANLLSLGGVPLVELMHLQAGTGLVSP 360
           AVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQANL +LGGV LVEL HLQAGTGLVSP
Sbjct: 301 AVKQIKVGPWNAQPQPFMGSMISEAAAKGMVAAQANLQNLGGVSLVELSHLQAGTGLVSP 360

Query: 361 GLIDVTAVSELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSAGILADSREDYEYFLA 420
           GLIDVTAV ELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSAGILADSR+DYEYFLA
Sbjct: 361 GLIDVTAVGELPDEEYFGPLLQLVRYSDFDQAIKLANQTRYGLSAGILADSRDDYEYFLA 420

Query: 421 RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASVEADAVSLPATL 480
           RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASVEADAVSLPA+L
Sbjct: 421 RIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAYPVASVEADAVSLPASL 480

Query: 481 SPGLTL 486
           SPGL+L
Sbjct: 481 SPGLSL 486


Lambda     K      H
   0.316    0.133    0.391 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1026
Number of extensions: 28
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 487
Length of database: 487
Length adjustment: 34
Effective length of query: 453
Effective length of database: 453
Effective search space:   205209
Effective search space used:   205209
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate 7023382 Shewana3_0612 (succinylglutamic semialdehyde dehydrogenase (RefSeq))
to HMM TIGR03240 (astD: succinylglutamate-semialdehyde dehydrogenase (EC 1.2.1.71))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR03240.hmm
# target sequence database:        /tmp/gapView.13779.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03240  [M=484]
Accession:   TIGR03240
Description: arg_catab_astD: succinylglutamate-semialdehyde dehydrogenase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                         Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   9.5e-249  811.9   2.4   1.1e-248  811.7   2.4    1.0  1  lcl|FitnessBrowser__ANA3:7023382  Shewana3_0612 succinylglutamic s


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7023382  Shewana3_0612 succinylglutamic semialdehyde dehydrogenase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  811.7   2.4  1.1e-248  1.1e-248       1     483 [.       3     485 ..       3     486 .. 1.00

  Alignments for each domain:
  == domain 1  score: 811.7 bits;  conditional E-value: 1.1e-248
                         TIGR03240   1 lfidGkwraGqGeslesldpvtqevlwqgkaasaaqvekavkaarkafpawarlsleeriavvkrfaelleeekeel 77 
                                       +fi+G+w+aG+G++++s++p+++e +w+g++a+a+qv++av aar+a  +w  l ++ r+++v+ + ++le +k+el
  lcl|FitnessBrowser__ANA3:7023382   3 HFIKGQWQAGKGHDVTSSNPANSEIIWRGQTATAEQVNAAVDAAREAQFDWFMLGFDGRLKIVEAYRSQLEANKAEL 79 
                                       69*************************************************************************** PP

                         TIGR03240  78 aeviaketgkplweartevasmvakvaisikayeertGekeseladakavlrhrphGvlavfGpynfpGhlpnGhiv 154
                                       ae+ia+etgkp+we++teva+m++k+ +s  ay++rtG++++++++++avlrh+phGv+avfGpynfpGhlpnGhiv
  lcl|FitnessBrowser__ANA3:7023382  80 AETIAQETGKPQWETATEVAAMIGKIGLSATAYNKRTGTEANDTPAGRAVLRHKPHGVVAVFGPYNFPGHLPNGHIV 156
                                       ***************************************************************************** PP

                         TIGR03240 155 pallaGntvvfkpseltplvaeetvklwekaGlpaGvlnlvqGaretGkalaaeedidGllftGssntGallhrqla 231
                                       pallaGntvvfkpseltp+vae +v lwekaGlpaGv+nlvqG+++tGkala+++++dGl+ftGss+tG+llh+q+a
  lcl|FitnessBrowser__ANA3:7023382 157 PALLAGNTVVFKPSELTPKVAELMVSLWEKAGLPAGVINLVQGEVDTGKALASHPQLDGLFFTGSSRTGHLLHQQYA 233
                                       ***************************************************************************** PP

                         TIGR03240 232 grpekilalelGGnnplvveevkdidaavhlivqsafisaGqrctcarrllvkdgaeGdallerlvevaerltvgky 308
                                       g+p kilale+GGnnpl+++ v+di+aavh+i+qsa+is+Gqrctcarrl v++g++Gdal+++lve  ++++vg +
  lcl|FitnessBrowser__ANA3:7023382 234 GHPGKILALEMGGNNPLIIKGVADIKAAVHDILQSAYISSGQRCTCARRLYVEQGEQGDALVAKLVEAVKQIKVGPW 310
                                       ***************************************************************************** PP

                         TIGR03240 309 daepqpflGavisekaakellaaqekllalggksllelkqleeeaalltpgiidvtevaevpdeeyfgpllkvlryk 385
                                       +a+pqpf+G++ise aak ++aaq++l++lgg sl+el++l+++++l++pg+idvt+v e+pdeeyfgpll+++ry+
  lcl|FitnessBrowser__ANA3:7023382 311 NAQPQPFMGSMISEAAAKGMVAAQANLQNLGGVSLVELSHLQAGTGLVSPGLIDVTAVGELPDEEYFGPLLQLVRYS 387
                                       ***************************************************************************** PP

                         TIGR03240 386 dfdealaeanntrfGlaaGllsddrelydkflleiraGivnwnkpltGassaapfGGiGasGnhrpsayyaadycay 462
                                       dfd+a++ an+tr+Gl+aG+l+d+r+ y++fl +iraGivnwnk++tGas+aapfGG+GasGnhr+sa+yaadycay
  lcl|FitnessBrowser__ANA3:7023382 388 DFDQAIKLANQTRYGLSAGILADSRDDYEYFLARIRAGIVNWNKQITGASGAAPFGGVGASGNHRASAFYAADYCAY 464
                                       ***************************************************************************** PP

                         TIGR03240 463 pvasleadslalpatlspGlk 483
                                       pvas+ead ++lpa+lspGl+
  lcl|FitnessBrowser__ANA3:7023382 465 PVASVEADAVSLPASLSPGLS 485
                                       *******************97 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (484 nodes)
Target sequences:                          1  (487 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 10.97
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources